A common problem in raising an antibody is the high background
cross-reactions to non-target proteins. One of the reasons is that
proteins share similar sequences. Certain sequences are
over-represented. For an example, searching a non-redundant mouse
protein database I found that the quadri-peptide SGSG is present in
the mouse proteome for 5197 times in 3170 proteins, and the
quadri-peptide ACWM is present for only 2 times in 2 proteins. If the
sequence you used for raising an antibody happens to contain an
over-represented sequence, it is likely a fraction of the antibody
will reacts with the over-represented sequences, therefore
cross-reacts with a large number of non-target proteins.
Chang Bioscience has introduced Abie Pro 3.0 to reduce this source of
cross-reactions. Abie Pro searches a proteome for over-represented
sequences and gives a user an option to select only peptides with few
over-represented sequences for antibody production. The online version
is available at
http://www.changbioscience.com/abie/abie.html
You are invited to try it. Critics, comments, and suggestions will be
especially appreciated.
Thanks.
Chang